pints-team/pints issues and pull requests

#1448 - Stan interface notebook is broken

Issue - State: closed - Opened by MichaelClerx over 2 years ago - 1 comment
Labels: bug

#1447 - Parallelisation fix for ABC Rejection

Pull Request - State: closed - Opened by phumtutum almost 3 years ago - 5 comments

#1446 - sample generative model

Issue - State: closed - Opened by martinjrobins almost 3 years ago - 2 comments
Labels: new method

#1445 - Issue 1443 explain

Pull Request - State: closed - Opened by rccreswell almost 3 years ago - 1 comment

#1444 - Issue 1443 multiple logpdfs

Pull Request - State: closed - Opened by rccreswell almost 3 years ago - 3 comments

#1443 - Optionally copy logpdfs before running mcmc

Issue - State: closed - Opened by rccreswell almost 3 years ago - 3 comments
Labels: question, code and design

#1442 - ABC SMC/PMC

Pull Request - State: closed - Opened by phumtutum almost 3 years ago - 17 comments

#1441 - Extended scatter search optimiser

Issue - State: closed - Opened by MichaelClerx almost 3 years ago
Labels: new method

#1440 - Added URL meta data to setup.py

Pull Request - State: closed - Opened by MichaelClerx almost 3 years ago - 2 comments

#1439 - Test on Python 3.10

Pull Request - State: closed - Opened by MichaelClerx almost 3 years ago - 4 comments

#1438 - Don't use the variable name "values" in the examples

Issue - State: closed - Opened by mirams almost 3 years ago
Labels: documentation

#1437 - Fix tiny docs typo

Pull Request - State: closed - Opened by chonlei almost 3 years ago - 1 comment

#1436 - Tiny typo in plot docs

Issue - State: closed - Opened by chonlei almost 3 years ago

#1435 - Update stan interface to pystan 3

Pull Request - State: closed - Opened by MichaelClerx almost 3 years ago - 22 comments

#1434 - Add testing on 3.10

Issue - State: closed - Opened by MichaelClerx almost 3 years ago - 1 comment
Labels: testing

#1433 - Drop support for Python 3.5

Pull Request - State: closed - Opened by MichaelClerx almost 3 years ago - 1 comment

#1432 - Added additional stochastic models[finished]

Pull Request - State: closed - Opened by phumtutum almost 3 years ago - 2 comments

#1431 - OptimisationController.set_parallel() no longer speeds up optimisation for CMAES

Issue - State: closed - Opened by HOLL95 about 3 years ago - 1 comment
Labels: bug

#1418 - Add some great cma-es visualisations in notebooks

Issue - State: closed - Opened by MichaelClerx about 3 years ago - 1 comment
Labels: documentation

#1416 - Create log-likelihoods for Binomial and Negative Binomial distributions

Issue - State: closed - Opened by I-Bouros about 3 years ago - 1 comment
Labels: feature

#1415 - I 1410 negbinom log priors

Pull Request - State: closed - Opened by I-Bouros about 3 years ago - 9 comments

#1414 - CMA-ES: Add option to re-enable its own stopping criteria

Issue - State: open - Opened by MichaelClerx about 3 years ago
Labels: feature

#1413 - ABC Routine

Pull Request - State: closed - Opened by phumtutum about 3 years ago - 12 comments
Labels: new method

#1412 - OptimisationController: Add method to store all points and evaluations in memory

Issue - State: closed - Opened by MichaelClerx about 3 years ago
Labels: feature

#1410 - Create log-priors for Binomial and Negative binomial distributions

Issue - State: closed - Opened by I-Bouros about 3 years ago - 1 comment
Labels: feature

#1405 - Wragged output methods

Pull Request - State: open - Opened by ben18785 over 3 years ago - 4 comments

#1404 - Allow simulation output to be cached

Issue - State: closed - Opened by MichaelClerx over 3 years ago - 2 comments
Labels: feature

#1402 - TransformedBoundaries and TransformedLogPrior don't override full interface

Issue - State: closed - Opened by MichaelClerx over 3 years ago - 3 comments
Labels: bug

#1401 - Require `sample_initial_points` function to produce samples in a list

Issue - State: open - Opened by ben18785 over 3 years ago
Labels: code and design

#1400 - NUTS / transform / Goodwin failing

Issue - State: open - Opened by ben18785 over 3 years ago
Labels: bug

#1396 - Use `sample_initial_points` for the majority of sampling-based notebooks

Issue - State: open - Opened by ben18785 over 3 years ago
Labels: documentation

#1393 - Create a changelog for sampling / optimisation initialisation PR

Issue - State: open - Opened by ben18785 over 3 years ago - 1 comment

#1382 - Allow PopulationMCMC to use different internal methods

Issue - State: closed - Opened by MichaelClerx over 3 years ago - 1 comment
Labels: feature, new method

#1378 - Log-normal log-likelihood

Pull Request - State: closed - Opened by ben18785 over 3 years ago - 2 comments

#1376 - Add more useful log likelihoods

Issue - State: open - Opened by ben18785 over 3 years ago - 10 comments
Labels: feature

#1372 - Is there a need for SingleOutputProblem and MultiOutputProblem?

Issue - State: closed - Opened by ben18785 over 3 years ago - 1 comment
Labels: question, code and design

#1364 - Formulate a policy for which Python 3.x versions to support

Issue - State: closed - Opened by MichaelClerx over 3 years ago - 1 comment
Labels: code and design, infrastructure

#1363 - "Getting started"

Issue - State: closed - Opened by MichaelClerx over 3 years ago
Labels: documentation

#1354 - Add argument to provide "context" for multiprocessing in evaluators... and controllers?

Issue - State: closed - Opened by MichaelClerx over 3 years ago
Labels: feature, question

#1344 - Hager_Zhang first commit

Pull Request - State: open - Opened by alisterde over 3 years ago - 3 comments

#1340 - Move open-ended issues to slack instead?

Issue - State: closed - Opened by MichaelClerx over 3 years ago - 1 comment

#1339 - Dram simplification (and addressing bug)

Pull Request - State: closed - Opened by ben18785 almost 4 years ago - 1 comment

#1338 - Interesting looking ODE models in DramAC paper

Issue - State: closed - Opened by ben18785 almost 4 years ago
Labels: science!

#1337 - Bug in DramACMC

Issue - State: closed - Opened by ben18785 almost 4 years ago

#1334 - I1300 pointwise log likelihoods

Pull Request - State: open - Opened by Rebecca-Rumney almost 4 years ago - 1 comment

#1333 - Update stan interface to use pystan 3

Issue - State: closed - Opened by ben18785 almost 4 years ago - 14 comments
Labels: priority, testing, infrastructure

#1332 - Intuition on samplers and optimisers

Issue - State: closed - Opened by DavAug almost 4 years ago
Labels: science!

#1330 - Matplotlib error on testing

Issue - State: closed - Opened by ben18785 almost 4 years ago
Labels: bug

#1328 - Add evaluateS1 method for HighDimensionalGaussianLogPDF

Issue - State: closed - Opened by ben18785 almost 4 years ago - 3 comments
Labels: feature

#1325 - Mistake in acceptance ratio in Emcee hammer

Issue - State: closed - Opened by ben18785 almost 4 years ago
Labels: bug

#1319 - MultiNest

Pull Request - State: open - Opened by ben18785 almost 4 years ago - 1 comment

#1318 - Parallel evaluation issue?

Issue - State: closed - Opened by ben18785 almost 4 years ago - 14 comments
Labels: bug

#1315 - To dos: redux

Issue - State: closed - Opened by ben18785 almost 4 years ago - 9 comments

#1314 - Optimise performance of NUTS

Issue - State: closed - Opened by DavAug almost 4 years ago - 11 comments

#1312 - Create a .sampler() method for nested controller

Issue - State: open - Opened by ben18785 almost 4 years ago
Labels: feature

#1304 - PyStan interface not seeded?

Issue - State: closed - Opened by MichaelClerx almost 4 years ago - 30 comments
Labels: testing

#1300 - Compute pointwise log-likelihood for each observation

Issue - State: closed - Opened by DavAug almost 4 years ago - 7 comments
Labels: feature

#1299 - Store energies for HMC samplers

Issue - State: closed - Opened by DavAug almost 4 years ago - 1 comment
Labels: feature

#1295 - Change-point tests

Pull Request - State: open - Opened by DavAug almost 4 years ago - 5 comments

#1294 - Create a functional testing module with tests for all methods

Issue - State: open - Opened by DavAug almost 4 years ago - 5 comments
Labels: testing

#1284 - Pull request template for merging in new methods

Pull Request - State: open - Opened by ben18785 almost 4 years ago - 1 comment

#1283 - Diagnostics module design

Issue - State: open - Opened by MichaelClerx almost 4 years ago - 19 comments
Labels: code and design

#1279 - Boundaries in transformation and boundaries classes: half-open vs open

Issue - State: open - Opened by chonlei almost 4 years ago
Labels: question

#1272 - Remove for-loop from `autocorrelate_negative`

Issue - State: closed - Opened by MichaelClerx about 4 years ago - 2 comments
Labels: easy win

#1267 - Eight schools notebook failing in daily test

Issue - State: closed - Opened by MichaelClerx about 4 years ago - 5 comments
Labels: bug

#1252 - Update emcee / mcmc hammer to "algorithm 3"

Issue - State: closed - Opened by MichaelClerx about 4 years ago
Labels: new method

#1248 - Hierarchical modelling

Issue - State: closed - Opened by DavAug about 4 years ago - 8 comments
Labels: feature

#1241 - Implement recycled HMC / NUTS steps

Issue - State: closed - Opened by ben18785 about 4 years ago
Labels: feature

#1232 - HierarchicalLogPrior class

Pull Request - State: open - Opened by MichaelClerx about 4 years ago - 1 comment

#1225 - Have a look at pakman

Issue - State: closed - Opened by MichaelClerx over 4 years ago
Labels: science!

#1223 - Have a look at SBStoat

Issue - State: closed - Opened by MichaelClerx over 4 years ago
Labels: science!

#1218 - Have a look at pypesto

Issue - State: closed - Opened by MichaelClerx over 4 years ago
Labels: science!

#1209 - Composed/Composite boundaries

Issue - State: closed - Opened by MichaelClerx over 4 years ago - 1 comment
Labels: feature

#1197 - Add Brent's derivative-free PRAXIS optimiser

Issue - State: closed - Opened by MichaelClerx over 4 years ago
Labels: new method

#1188 - Have a look at sktime

Issue - State: closed - Opened by MichaelClerx over 4 years ago
Labels: science!

#1187 - Add more transformation functions

Issue - State: closed - Opened by chonlei over 4 years ago
Labels: feature

#1181 - Diagnostic plots for detecting autoregressive and non-stationary noise

Issue - State: closed - Opened by rccreswell over 4 years ago - 3 comments
Labels: feature

#1171 - Interface to see order of parameters in LogPDFs

Issue - State: closed - Opened by DavAug over 4 years ago - 2 comments
Labels: feature, new method

#1162 - Add model selection in Pints

Issue - State: closed - Opened by chonlei over 4 years ago
Labels: feature, documentation

#1161 - Look into ArviZ

Issue - State: closed - Opened by chonlei over 4 years ago
Labels: science!

#1149 - I1083 l bfgs optimiser

Pull Request - State: open - Opened by alisterde over 4 years ago - 9 comments

#1148 - Add notebook showing sensitivity/jacobian calculations via sympy lambidy

Issue - State: closed - Opened by MichaelClerx over 4 years ago - 8 comments
Labels: documentation

#1145 - Surface using of linear interpolation on the delaunay triangulation

Issue - State: closed - Opened by MichaelClerx over 4 years ago
Labels: feature

#1140 - "Optimal" thinning and burn-in

Issue - State: closed - Opened by MichaelClerx over 4 years ago - 1 comment
Labels: feature

#1138 - I1137 horowitz langevin mcmc

Pull Request - State: open - Opened by DavAug over 4 years ago - 17 comments

#1134 - HierarchicalModelLogPDF

Issue - State: closed - Opened by DavAug over 4 years ago - 8 comments
Labels: feature

#1133 - Tolerances for adaptive step size solvers

Issue - State: closed - Opened by MichaelClerx over 4 years ago - 2 comments
Labels: documentation, student-project

#1128 - R star MCMC convergence metric

Issue - State: closed - Opened by ben18785 over 4 years ago - 1 comment
Labels: feature

#1124 - Add Interface / example notebook with numpyro

Issue - State: closed - Opened by ben18785 over 4 years ago - 19 comments
Labels: documentation

#1117 - Propp-Wilson algorithm

Issue - State: closed - Opened by MichaelClerx almost 5 years ago - 3 comments
Labels: new method

#1105 - Add some more simple gradient descent methods

Issue - State: closed - Opened by MichaelClerx almost 5 years ago - 1 comment
Labels: new method, good first issue

#1100 - Move unit testing into main.py ?

Issue - State: closed - Opened by MichaelClerx almost 5 years ago
Labels: code and design, priority, testing

#1092 - SHGO optimiser

Issue - State: closed - Opened by ben18785 almost 5 years ago - 1 comment
Labels: new method

#1073 - Unit testing with optional extras

Issue - State: closed - Opened by MichaelClerx almost 5 years ago
Labels: testing

#1067 - Generic Stochastic Model

Pull Request - State: open - Opened by jarthur36 almost 5 years ago - 4 comments

#1056 - Dynamic exiting of sampling but preserving the sampler(s)' state

Issue - State: closed - Opened by ben18785 almost 5 years ago - 5 comments
Labels: feature, student-project

#1055 - ABC-SMC

Pull Request - State: closed - Opened by jarthur36 almost 5 years ago - 5 comments
Labels: new method

#1048 - Make method that allows comparison of estimates from a number of different samplers / runs

Issue - State: closed - Opened by ben18785 almost 5 years ago - 2 comments
Labels: feature

#1046 - Neural network gradient HMC

Issue - State: closed - Opened by ben18785 almost 5 years ago - 2 comments
Labels: new method

#1045 - Generalised HMC with neural networks

Issue - State: closed - Opened by ben18785 almost 5 years ago - 2 comments
Labels: new method

GitHub / pints-team/pints issues and pull requests